Simulating surface-mediated proton transport at decorated surfaces
EMSL Project ID
35403
Abstract
Proton translocation in biological membrane proton pumps is an essential part of many bio-energetic processes. Many membrane proton pumping proteins transport protons in a very efficient manner. The proton conductance via such proteins can be one order of magnitude faster than proton diffusion in bulk even when there exists a proton gradient against which the protons need to be transported. This fast proton transport requires an efficient proton uptake from the environment (e.g. the cellular solution). The proton uptake process is essentially a directed proton transfer near the protein-membrane / bulk solution interface. Understanding the proton diffusion mechanism near surfaces with different chemical composition (e.g. the protein/membrane surface) is not only important for deeper insight in basic biological phenomena but also has relevance in related application fields like the design of new nanoscale instrument like proton filer/pumps or more efficient hydrogen-fuel cells. In this project, we will extend our previous study on the proton-collecting antenna effect at protein surfaces to the study of surface-mediated proton transport at surfaces with different properties (e.g. hydrophobic surfaces, hydrophilic surfaces) and with different decorations (e.g. amino acid residues with different pKa). We hope to find the relation between proton uptake rate and the surface properties and mechanism of proton diffusion/uptake near different surfaces at atomic level. The main computational technique that will be applied in this project is the Q-HOP molecular dynamics simulation, which has been developed in the Helms' group and has been implemented in the NWChem package.
Project Details
Project type
Capability Research
Start Date
2009-10-01
End Date
2012-09-30
Status
Closed
Released Data Link
Team
Principal Investigator
Team Members
Related Publications
Gu W, B Zhou, T Geyer, MC Hutter, H Fang, and VH Helms. 2011. "Design of a Gated Molecular Proton Channel." Angewandte Chemie International Edition 50(3):768-771. doi:10.1002/anie.201002564
Herzog E, W Gu, HD Juhnke, AH Haas, W Mantele, J Simon, VH Helms, and CRD Lancaster . 2012. "Hydrogen-Bonded Networks Along and Bifurcation of the E-Pathway in Quinol: Fumarate Reductase." Biophysical Journal 103:1305-1314. doi:10.1016/j.bpj.2012.07.037